either double bond is gone after indigoLoad of hydrazones R-N(H)-N=C-R1

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Karen Karapetyan

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Apr 3, 2013, 4:04:52 PM4/3/13
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Another case when either bond is gone after loading to Indigo

--------------------

  Symyx   03191313102D 1   1.00000     0.00000     0

 19 20  0     0  0            999 V2000
    8.6583   -1.6667    0.0000 N   0  3  0  0  0  0           0  0  0
    8.6458   -4.2542    0.0000 N   0  3  0  0  0  0           0  0  0
    7.4958   -2.3542    0.0000 C   0  0  0  0  0  0           0  0  0
    9.8833   -2.3667    0.0000 C   0  0  0  0  0  0           0  0  0
    9.8458   -3.5917    0.0000 C   0  0  0  0  0  0           0  0  0
    7.4958   -3.5542    0.0000 C   0  0  0  0  0  0           0  0  0
    4.3193   -4.5309    0.0000 C   0  0  0  0  0  0           0  0  0
    8.6958   -0.2875    0.0000 O   0  5  0  0  0  0           0  0  0
    6.2958   -1.6667    0.0000 C   0  0  0  0  0  0           0  0  0
    8.6583   -5.6292    0.0000 O   0  5  0  0  0  0           0  0  0
    5.2708   -2.3542    0.0000 N   0  0  0  0  0  0           0  0  0
    4.1523   -3.1924    0.0000 N   0  0  0  0  0  0           0  0  0
    5.4450   -4.9927    0.0000 O   0  0  0  0  0  0           0  0  0
    3.2210   -5.3639    0.0000 O   0  0  0  0  0  0           0  0  0
   11.0458   -1.6667    0.0000 C   0  0  0  0  0  0           0  0  0
   11.0333   -4.2542    0.0000 C   0  0  0  0  0  0           0  0  0
    3.4274   -6.7051    0.0000 C   0  0  0  0  0  0           0  0  0
   12.1875   -2.3542    0.0000 C   0  0  0  0  0  0           0  0  0
   12.1875   -3.5917    0.0000 C   0  0  0  0  0  0           0  0  0
  2  5  1  0     0  0
  3  1  2  0     0  0
  4  1  1  0     0  0
  5  4  2  0     0  0
  6  3  1  0     0  0
  7 12  1  0     0  0
  8  1  1  0     0  0
  9  3  1  0     0  0
 10  2  1  0     0  0
 11  9  2  3     0  0
 12 11  1  0     0  0
 13  7  2  0     0  0
 14  7  1  0     0  0
 15  4  1  0     0  0
 16  5  1  0     0  0
 17 14  1  0     0  0
 18 15  2  0     0  0
 19 18  1  0     0  0
  6  2  2  0     0  0
 19 16  2  0     0  0
M  CHG  4   1   1   2   1   8  -1  10  -1
M  END
-------------------

Mikhail Rybalkin

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Apr 3, 2013, 4:13:57 PM4/3/13
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In this case such behavior is expected because the Nitrogen substituent is one the same line with double bond. It means that even without "either" mark it is not possible to determine cis-trans configuration and so it is not necessary to set either double bond. I simply moved the Nitrogen and now everything is fine.

Indigo tells that SMILES for your original molecule is [N+]1([O-])C2C=CC=CC=2[N+](=CC=1C=NNC(OC)=O)[O-] and this is fine because there is no cis-trans flags in this SMILES.
either.mol

Karen Karapetyan

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Apr 3, 2013, 4:20:27 PM4/3/13
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I agree that layout is not good and I understand that N-N=C are lined up but still molfile explicitly gives stereo type "either" for that double bond. 
Though smiles are fine it seems to me that users would expect that either bond stay in tact in indigo.molfile() as well. 

Karen Karapetyan

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Apr 3, 2013, 4:22:55 PM4/3/13
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Another argument for keeping the "either" double bond in molfile is that it would make difference at layout. If layout arranges that double bond stereo as cis/trans then it will show up in molfile as cis/trans.

Mikhail Rybalkin

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Apr 3, 2013, 4:27:52 PM4/3/13
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I agree with your argument about the layout procedure. If you do a layout then either mark is not saved and you gets cis-trans configuration (I checked and this happens in this case). So this behavior a bug. We will fix it!

Mikhail Rybalkin

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Apr 4, 2013, 5:56:55 AM4/4/13
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Hi Ken,

Could you check the attached version of Indigo .NET? Now either double bond flag is preserved in such case too.

Best regards,
Mikhail
indigo-dotnet-1.1.9-win.zip
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